Удалить из индекса все файлы, что были удалены не через git.

$ rm b d foo/baz
$ git status

# On branch master
# Changed but not updated:
#   (use "git add/rm <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#       deleted:    b
#       deleted:    d
#       deleted:    foo/baz
#
no changes added to commit (use "git add" and/or "git commit -a")

$ git add -u
$ git status

# On branch master
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#       deleted:    b
#       deleted:    d
#       deleted:    foo/baz
#